Abstract 3369: Epigenetic DNA methylation profiling of triple negative breast cancer: a quantitative NGS approach

Abstract

Abstract Triple negative breast cancer (TNBC) is an aggressive disease with a high degree of genomic instability. TNBC patients have poor prognosis and the risk of metastasis and death is increased for women who relapse within four years of treatment compared to other breast cancer subtypes. Currently, there are no reliable prognostic markers to identify which population is at risk for early relapse and the molecular mechanism for disease recurrence is not well understood. Epigenetic changes, especially DNA methylation, are common in breast cancer and have been found to be associated with increased metastatic capability. Therefore, the methylation states of genes in TNBC tumors compared to non-tumor breast tissue was examined in order to identify potential biomarkers and therapeutic targets in TNBC. Matched tumor and adjacent non-tumor tissue from patients with TNBC were obtained following surgical resection and genomic DNA was extracted. Epigenetic profiling of TNBC tumors and non-tumor tissue was performed using a highly sensitive and quantitative analytics platform, which utilizes methylation sensitive restriction endonucleases to detect changes in methylation of CpG sites. Millions of CpG sites exist within the human genome and many of these are altered with tumor formation and progression, therefore, changes in methylation profiles of CpG sites may be useful as a diagnostic and/or prognostic biomarker in TNBC patients. Non-metric multidimensional scaling ordination analysis of the CpG sites revealed highly distinct methylation patterns between tumor and non-tumor tissue. Approximately 326 sites had a significant methylation score difference (p&lt0.0025) between TNBC tumor and non-tumor tissue, with most of the CpG sites having greater than 2-fold change in methylation status. Analysis of functional gene classes using KEGG classifiers revealed a significant change in methylation patterns of genes involved in response to infections and other immune related functions. Additionally, the top ten genes with hyper- or hypomethylated sites within TNBC tumors when compared to non-tumor tissue were identified. Interestingly, Gli-1 was one of the top hypomethylated genes. Gli-1 has been shown in our lab and others to have significance in chemoresistance and recurrence in TNBC patients. Immunohistochemical analysis of TNBC tumors revealed Gli-1 overexpression in TNBC tumors compared to non-tumor tissue. Expression levels of Gli-1 in TNBC tumors correlated with stage (p&lt0.001) and recurrence free (p&lt0.0213) and overall survival (p&lt0.017). Thus, analysis of CpG methylated sites in TNBC tumors and non-tumor tissue revealed differences in epigenetic profiles allowing for distinction between tumor and non-tumor tissue. Genes in TNBC tumors with significant changes in methylation status may be potential candidate genes that serve as a diagnostic or prognostic biomarker for TNBC. Citation Format: Kimberly M. Arnold, Adam G. Marsh, Jennifer Sims-Mourtada. Epigenetic DNA methylation profiling of triple negative breast cancer: a quantitative NGS approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3369. doi:10.1158/1538-7445.AM2017-3369